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update dependencies

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-04-02 16:05:09 +02:00
parent cee64ef050
commit 07bdd61241
15 changed files with 172 additions and 221 deletions
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25
tests/testthat/test-first_isolates.R
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@@ -7,7 +7,6 @@ test_that("keyantibiotics work", {
expect_false(key_antibiotics_equal("SSS", "SIS", ignore_I = FALSE))
})
test_that("guess_bactid works", {
expect_equal(guess_bactid("E. coli"), "ESCCOL")
expect_equal(guess_bactid("Escherichia coli"), "ESCCOL")
@@ -15,9 +14,23 @@ test_that("guess_bactid works", {
test_that("first isolates work", {
# septic_patients contains 1960 out of 2000 first isolates
expect_equal(sum(first_isolate(septic_patients,
"date",
"patient_id",
"bactid",
info = FALSE)), 1960)
septic_ptns <- septic_patients
expect_equal(sum(first_isolate(tbl = septic_ptns,
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
info = FALSE)), 1960)
# septic_patients contains 1962 out of 2000 first weighted isolates
septic_ptns$keyab <- suppressWarnings(key_antibiotics(septic_ptns))
expect_equal(
suppressWarnings(sum(
first_isolate(tbl = septic_ptns,
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
col_keyantibiotics = "keyab",
type = "keyantibiotics",
info = TRUE))),
1962)
})